[FieldTrip] warping from MNI to individual subjects

[Meike Schweisfurth]

Dear Julian!
Thanks for your help!
I guess it has been only a visualisation problem, it seems to be fine now!
Thanks anyway!
Meike


2014-04-01 15:12 GMT+02:00 Julian Keil <julian.keil at gmail.com>:

> Dear Meike,
>
> I'm not sure if this relates to your problem, but I had - possibly similar
> - issues with the warped grid and the template being 90° rotated.
> My problem was due to an error during the realignment of the MRI.
> Did you check whether the realignment works and whether your different
> coordinate systems make sense?
>
> Could you also maybe attach a picture of your exchanged axes? At least for
> me it's hard to image how this looks.
>
> Best,
>
> Julian
>
>
> ********************
> *Dr. Julian Keil*
>
> AG Multisensorische Integration
> Psychiatrische Universitätsklinik
> der Charité im St. Hedwig-Krankenhaus
> Große Hamburger Straße 5-11, Raum E 307
> 10115 Berlin
>
> Telefon: +49-30-2311-1879
> Fax:        +49-30-2311-2209
>
> http://psy-ccm.charite.de/forschung/bildgebung/ag_multisensorische_integration
>
> Am 01.04.2014 um 14:12 schrieb Meike Schweisfurth:
>
>  Dear Fieldtrippers!
> As newbie I have another question, now concerning the warping from MNI to
> individual subjects.
> Using the below code (the first part almost entirely from
> http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space),
> I get first the template and then apply the grid to the individual
> subjects.
> However, in later on analysis step it turned out that while the subjects
> where nicely similar positioned, the template position is entirely
> different, as it is was even axes were exchanged...
> Does anybody know what could be the reason and how to change it?
> Thanks for any suggestions!
> Best, Meike
>
>
> % NOTE: the path to the template file is user-specific
> template =
> ft_read_mri('fieldtrip/fieldtrip-20140316/external/spm8/templates/T1.nii');
> template.coordsys = 'spm'; % so that FieldTrip knows how to interpret the
> coordinate system
>
> % segment the template brain and construct a volume conduction model (i.e.
> head model): this is needed
> % for the inside/outside detection of voxels.
> cfg          = [];
> template_seg = ft_volumesegment(cfg, template);
>
> cfg          = [];
> cfg.method   = 'singleshell';
> template_vol = ft_prepare_headmodel(cfg, template_seg);
> template_vol = ft_convert_units(template_vol, 'cm'); % Convert the vol to
> cm, since the grid will also be expressed in cm
>
> % construct the dipole grid in the template brain coordinates
> % the source units are in cm
> % the negative inwardshift means an outward shift of the brain surface for
> inside/outside detection
> cfg = [];
> cfg.grid.xgrid  = -20:1:20;
> cfg.grid.ygrid  = -20:1:20;
> cfg.grid.zgrid  = -20:1:20;
> cfg.grid.unit   = 'cm';
> cfg.grid.tight  = 'yes';
> cfg.inwardshift = -1.5;
> cfg.vol        = template_vol;
> template_grid  = ft_prepare_sourcemodel(cfg);
> save('../analysis/MEG/source_analysis/MNI','template_grid','template_vol','template_seg','template')
>
> % make a figure with the template head model and dipole grid
> figure
> hold on
> ft_plot_vol(template_vol, 'facecolor', 'cortex', 'edgecolor',
> 'none');alpha 0.5; camlight;
> ft_plot_mesh(template_grid.pos(template_grid.inside,:));
> else
> load('../analysis/MEG/source_analysis/MNI','template_grid','template_vol','template_seg','template')
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>      SUBJECTS={    'VP02'    'VP03'    'VP04'    'VP05'    'VP06'
> 'VP07'    'VP08'    'VP09'    'VP11'    'VP12'    'VP13' 'VP14'
> 'VP15'    'VP16'    'VP17'    'VP18'}
>
> for SUBJI=SUBJECTS
>     SUBJ=SUBJI{1};
> % read the single subject anatomical MRI
> load(['..*/analysis/MEG/source_analysis/*',SUBJ,'/mri']);  %Has been
> processed to CFT coordinates before
> load(['..*/analysis/MEG/source_analysis/*',SUBJ,'/segmentedmri']);
>
>
> cfg = [];
> cfg.method = 'singleshell';
> vol = ft_prepare_headmodel(cfg, segmentedmri);
>
> % create the subject specific grid, using the template grid that has just
> been created
> cfg = [];
> cfg.grid.warpmni   = 'yes';
> cfg.grid.template  = template_grid;
> cfg.grid.nonlinear = 'yes'; % use non-linear normalization
> cfg.mri            = mri_ra;
> grid               = ft_prepare_sourcemodel(cfg);
>
> % make a figure of the single subject headmodel, and grid positions
> figure;
> ft_plot_vol(vol, 'edgecolor', 'none'); alpha 0.4; %camlight
> ft_plot_mesh(grid.pos(grid.inside,:));
>
> save(['..*/analysis/MEG/source_analysis/*',SUBJ,'/MNIgrid'],'grid','vol')
> end
>
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